{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:46:16Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.2, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0956f-7a0b-7852-8104-f206c6dc267f\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: OPRK1\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 1001 registere", "usd": 0.0, "recall": true }, "codex": { "seconds": 70.0, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0956f-7a06-71a2-8c97-e646f4c1d685\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: OPRK1\nRegistry id: vr.tr.oprk1\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContext for " } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:57:13+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:26+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14897645", "registryId": "vr.tr.oprk1", "name": "OPRK1", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14897645/", "model": { "registry_id": "vr.tr.oprk1", "name": "OPRK1", "purpose": "Enable an agent to identify OPRK1, distinguish its gene identity from its receptor product, and assess expression, variation and functional evidence in a specified biological context.", "definition": "OPRK1 is the human gene encoding the kappa opioid receptor, a seven-transmembrane G protein-coupled receptor activated by endogenous dynorphin peptides and involved in modulating neuronal signalling.", "scope_statement": "Provisionally interpret vr.tr.oprk1 as the human protein-coding gene OPRK1, which encodes the kappa-type opioid receptor, following [NCBI Gene 4986](https://www.ncbi.nlm.nih.gov/gene/4986); own its identity and evidence-bearing relationships to transcripts, receptor products and observations, pending confirmation of the registry's intended species and gene-versus-protein boundary.", "in_scope": [ "Species-qualified OPRK1 identity and reference sequence mappings", "Genomic variants and their transcript-dependent consequences", "OPRK1 transcript expression and its relationship to receptor abundance", "Links from encoded receptor products to binding and signaling observations", "Evidence needed to attribute an experimental effect specifically to OPRK1" ], "out_of_scope": [ "Independent models of opioid ligands and pharmaceutical formulations", "Complete models of other opioid receptor genes", "Whole-organism models of pain, addiction or mood", "Patient diagnosis and treatment selection", "General laboratory protocols and instrument operation", "Separate publication of receptor products or orthologs without resolving registry coverage" ], "distinguishing_features": [ "Resolve an identifier to OPRK1 in a named species; the symbol alone does not establish organism identity.", "Distinguish a genomic accession from an OPRK1 transcript accession and an encoded receptor protein accession before attaching observations.", "Require sequence or authoritative identifier mapping to distinguish OPRK1 from OPRM1, OPRD1 and OPRL1.", "Treat KOR or KOP labels as candidate receptor aliases requiring identity resolution, rather than proof that a record describes the gene.", "Distinguish endogenous OPRK1 from tagged, mutated or overexpressed constructs before transferring functional conclusions." ], "characteristics": [ { "name": "Biological entity level", "kind": "category", "unit_or_values": "gene locus | allele | transcript | encoded protein | experimental construct", "why_it_matters": "Prevents measurements of receptor behavior from being represented as physical states of a gene." }, { "name": "Organism identity", "kind": "relation", "unit_or_values": "Taxonomy identifier and organism name", "why_it_matters": "Separates human OPRK1 from orthologous genes and limits cross-species inference." }, { "name": "Reference sequence context", "kind": "relation", "unit_or_values": "Genome assembly, accession version, coordinates and strand", "why_it_matters": "Makes locus and variant descriptions reproducible." }, { "name": "Transcript-to-product mapping", "kind": "relation", "unit_or_values": "Versioned transcript accession linked to versioned protein accession", "why_it_matters": "Identifies the molecular product relevant to a consequence or functional assay." }, { "name": "OPRK1 transcript abundance", "kind": "measurement", "unit_or_values": "TPM, counts or assay-specific relative expression with normalization", "why_it_matters": "Supports expression comparisons only when tissue, method and normalization are compatible." }, { "name": "Encoded receptor localization", "kind": "state", "unit_or_values": "Surface-detected | intracellular-detected | mixed | undetected | unresolved, with method", "why_it_matters": "Separates receptor availability from transcript abundance." }, { "name": "Variant consequence", "kind": "category", "unit_or_values": "Reference-dependent consequence annotation plus experimental support status", "why_it_matters": "Separates predicted sequence effects from demonstrated changes in OPRK1 function." }, { "name": "Receptor response measurement", "kind": "measurement", "unit_or_values": "Endpoint-specific units; concentration in mol/L where applicable; comparator and uncertainty required", "why_it_matters": "Prevents binding affinity, response potency and response magnitude from being conflated." } ], "affordances": [ "Resolve an OPRK1 label to a species-qualified gene, transcript or receptor record.", "Map an observed sequence variant onto an explicitly versioned OPRK1 reference.", "Compare OPRK1 expression observations with compatible biological and analytical contexts.", "Trace a receptor assay result back to the OPRK1 sequence and construct tested.", "Evaluate whether genetic and pharmacological controls support OPRK1-specific attribution.", "Flag unsupported transfers between species, molecular products or experimental systems." ], "agent_conduct": { "may": [ "Describe OPRK1 and the kappa opioid receptor it encodes, citing sources.", "Report what a variant or expression result shows, with its source and limits." ], "must_not": [ "Interpret a person's OPRK1 variant as predicting addiction or behaviour.", "Share a person's genetic data without consent.", "Recommend drugs acting on this receptor to a person.", "Assist in obtaining controlled substances that act on opioid receptors outside lawful channels." ], "requires_human": [ "Using genetic results in clinical or treatment decisions.", "Research on patient samples without documented consent." ] }, "ethics": { "considerations": [ "Genetic links to addiction can stigmatize people if overstated.", "Drugs acting on opioid receptors can be misused and cause harm." ], "affected_parties": [ "People with genetic test results", "People living with addiction", "Patients" ] }, "owners": { "steward": "The person whose genome carries it; laboratories and biobanks hold sequence records.", "master_systems": [ "Gene and variant databases" ] }, "visual_identification": [ "Not visible; known from sequence data and receptor assays.", "Identified by its approved gene symbol and genomic location." ], "failure_modes_and_hazards": [ "Overinterpretation of variant associations.", "Privacy breaches of genetic data." ], "standards_and_regulation": [ "Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol." ], "what_it_is_for": [ "The human OPRK1 gene is encountered in genetic and gene expression studies of neuronal signalling and opioid receptor biology.", "It provides a reference for examining sequence variation and transcript expression in relation to the encoded kappa opioid receptor." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14897645: OPRK1", "url": "https://www.wikidata.org/wiki/Q14897645", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Κ-opioid receptor", "url": "https://en.wikipedia.org/wiki/%CE%9A-opioid_receptor", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "oprk1-identity-and-boundaries", "name": "OPRK1 identity and boundaries", "description": "Resolve which biological entity the registry name denotes.", "rationale": "OPRK1 can label gene records and receptor-related materials, while the registry supplies no definition.", "layers": [ { "id": "species-and-locus", "name": "Species and locus", "description": "Establish organism-qualified identity before integrating observations.", "findings": [ { "id": "authoritative-oprk1-mapping", "name": "Authoritative OPRK1 mapping", "description": "Require the registry record to resolve to an authoritative gene identifier and organism.", "questions": [ { "text": "Which source identifier originally placed OPRK1 in vr.tr.oprk1, and which organism does it specify?", "kind": "provenance", "id": "authoritative-oprk1-mapping-q01" }, { "text": "Does that source identify a gene locus, a receptor protein or a broader cross-species concept?", "kind": "boundary", "id": "authoritative-oprk1-mapping-q02" } ] } ] }, { "id": "gene-product-separation", "name": "Gene-product separation", "description": "Keep aliases and encoded products connected without treating them as identical entities.", "findings": [ { "id": "receptor-alias-resolution", "name": "Receptor alias resolution", "description": "Record whether each OPRK1, KOR or KOP usage denotes DNA, RNA, protein or experimental material.", "questions": [ { "text": "What molecular entity does each alias denote in the source being interpreted?", "kind": "definition", "id": "receptor-alias-resolution-q01" }, { "text": "Does an existing registry or world model already own the kappa-type opioid receptor concept?", "kind": "boundary", "id": "receptor-alias-resolution-q02" } ] } ] } ] }, { "id": "oprk1-sequence-and-products", "name": "OPRK1 sequence and products", "description": "Connect genomic references, transcripts and translated products.", "rationale": "Variant interpretation and receptor experiments require an explicit OPRK1 sequence context.", "layers": [ { "id": "genomic-reference", "name": "Genomic reference", "description": "Anchor locus and allele descriptions to reproducible coordinates.", "findings": [ { "id": "reference-dependent-variation", "name": "Reference-dependent variation", "description": "Keep observed OPRK1 alleles separate from consequence predictions.", "questions": [ { "text": "Which assembly, accession version and allele representation define the observed OPRK1 variant?", "kind": "definition", "id": "reference-dependent-variation-q01" }, { "text": "Which variant consequences are predicted, and which have direct experimental support?", "kind": "provenance", "id": "reference-dependent-variation-q02" } ] } ] }, { "id": "transcripts-and-translation", "name": "Transcripts and translation", "description": "Resolve the products relevant to each observation.", "findings": [ { "id": "product-specific-evidence", "name": "Product-specific evidence", "description": "Track transcript and protein accessions, including evidence for alternative products; NCBI reports alternative transcripts and translational readthrough for OPRK1. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/4986)", "questions": [ { "text": "Which transcript and protein sequence were measured or expressed in the cited experiment?", "kind": "provenance", "id": "product-specific-evidence-q01" }, { "text": "What evidence establishes the relevant alternative or readthrough product in the biological context under study?", "kind": "measurement", "id": "product-specific-evidence-q02" } ] } ] } ] }, { "id": "oprk1-expression-and-receptor-availability", "name": "OPRK1 expression and receptor availability", "description": "Distinguish transcription from the presence and accessibility of the encoded receptor.", "rationale": "An OPRK1 RNA signal alone cannot establish how much functional receptor is available.", "layers": [ { "id": "transcript-detection", "name": "Transcript detection", "description": "Qualify OPRK1 expression by sample composition and assay sensitivity.", "findings": [ { "id": "contextualized-rna-abundance", "name": "Contextualized RNA abundance", "description": "Attach tissue, cell type, sampling conditions and normalization to expression observations.", "questions": [ { "text": "Which cells or tissue contributed the OPRK1 RNA measurement, and was the sample mixed or cell-resolved?", "kind": "provenance", "id": "contextualized-rna-abundance-q01" }, { "text": "What normalization, detection limit and transcript specificity govern the reported abundance?", "kind": "measurement", "id": "contextualized-rna-abundance-q02" } ] } ] }, { "id": "protein-detection-and-location", "name": "Protein detection and location", "description": "Assess whether the encoded receptor is detected and accessible in the measured system.", "findings": [ { "id": "validated-receptor-availability", "name": "Validated receptor availability", "description": "Require receptor-specific detection and distinguish surface-associated from intracellular signal.", "questions": [ { "text": "What controls establish that the detected protein signal comes from the OPRK1 product?", "kind": "provenance", "id": "validated-receptor-availability-q01" }, { "text": "Does the assay quantify total receptor, surface receptor or ligand-accessible receptor?", "kind": "measurement", "id": "validated-receptor-availability-q02" } ] } ] } ] }, { "id": "oprk1-linked-receptor-function", "name": "OPRK1-linked receptor function", "description": "Attach binding and signaling observations to the encoded product actually tested.", "rationale": "Functional conclusions require separation of ligand binding, downstream response and receptor identity.", "layers": [ { "id": "ligand-recognition", "name": "Ligand recognition", "description": "Record product-specific ligand interactions and their experimental limits.", "findings": [ { "id": "binding-and-selectivity", "name": "Binding and selectivity", "description": "The human reference receptor recognizes dynorphins; individual binding and selectivity claims still require assay-specific evidence. [UniProt P41145](https://www.uniprot.org/uniprotkb/P41145/entry)", "questions": [ { "text": "Which ligand, OPRK1 product and assay conditions support the reported binding measurement?", "kind": "measurement", "id": "binding-and-selectivity-q01" }, { "text": "Which other opioid receptors were tested before describing the interaction as kappa-selective?", "kind": "boundary", "id": "binding-and-selectivity-q02" } ] } ] }, { "id": "signaling-response", "name": "Signaling response", "description": "Separate receptor engagement from the downstream endpoint measured.", "findings": [ { "id": "endpoint-specific-function", "name": "Endpoint-specific function", "description": "Represent each response with its endpoint, baseline, time course and experimental system.", "questions": [ { "text": "Which signaling endpoint was measured, and what were its baseline, reference response and observation time?", "kind": "measurement", "id": "endpoint-specific-function-q01" }, { "text": "What evidence connects the response to the specified OPRK1 product rather than another target or assay artifact?", "kind": "provenance", "id": "endpoint-specific-function-q02" } ] } ] } ] }, { "id": "oprk1-perturbation-and-inference", "name": "OPRK1 perturbation and inference", "description": "Assess what experiments and associations justify concluding about OPRK1.", "rationale": "Sequence changes, receptor-directed compounds and phenotype associations provide different strengths of attribution.", "layers": [ { "id": "experimental-attribution", "name": "Experimental attribution", "description": "Evaluate OPRK1-directed perturbations against relevant controls.", "findings": [ { "id": "perturbation-specificity", "name": "Perturbation specificity", "description": "Track the target sequence, altered product and controls behind a claimed OPRK1-dependent effect.", "questions": [ { "text": "Did the intervention alter OPRK1 DNA, RNA abundance, receptor abundance or receptor activity?", "kind": "definition", "id": "perturbation-specificity-q01" }, { "text": "Which rescue, independent perturbation or receptor-comparison experiment would resolve the remaining attribution uncertainty?", "kind": "action", "id": "perturbation-specificity-q02" } ] } ] }, { "id": "phenotype-and-transfer", "name": "Phenotype and transfer", "description": "Bound conclusions drawn from genetic associations and model systems.", "findings": [ { "id": "limits-of-oprk1-interpretation", "name": "Limits of OPRK1 interpretation", "description": "Keep association, experimental causation and transfer to another biological context explicitly separate.", "questions": [ { "text": "Does the phenotype evidence concern an OPRK1 variant, expression change or receptor perturbation, and what alternatives remain?", "kind": "provenance", "id": "limits-of-oprk1-interpretation-q01" }, { "text": "What evidence permits transferring the conclusion across species, cell systems or endogenous versus engineered expression?", "kind": "boundary", "id": "limits-of-oprk1-interpretation-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The missing sense leaves gene versus protein identity unresolved; this description interprets the uppercase symbol as the human gene.", "OPRK1 is a biological gene designation, so the batch's device-oriented guidance does not apply.", "This is recall only; species, transcript variants and database accession identifiers should be checked before publication." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of OPRK1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "HGNC gene symbol", "value_or_pattern": "OPRK1", "note": "The approved human gene symbol; the encoded protein is commonly called the kappa opioid receptor or KOR." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of OPRK1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Research on opioid receptor signalling and endogenous dynorphin function.", "Drug discovery targeting pain and itch.", "Research on stress, reward and addiction." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of OPRK1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Some centrally acting kappa opioid receptor agonists can produce dysphoria and sedation; these are pharmacological effects rather than hazards of the gene itself.", "Confusing the gene with its encoded receptor can lead to incorrect interpretation of expression, binding and functional assay results." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of OPRK1 this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Kappa opioid receptor", "difference": "The receptor is the protein encoded by OPRK1; OPRK1 denotes the gene." }, { "name": "OPRM1", "difference": "Encodes the mu opioid receptor rather than the kappa opioid receptor." }, { "name": "OPRD1", "difference": "Encodes the delta opioid receptor rather than the kappa opioid receptor." }, { "name": "PDYN", "difference": "Encodes prodynorphin, a precursor of endogenous receptor ligands, rather than the receptor." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of OPRK1 this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry's originating identifier designate human OPRK1, its receptor product or a species-independent concept?", "Does an existing world model already cover this gene or receptor, requiring linkage instead of a separate publication?", "Which transcript and protein reference versions should anchor the model, and which alternative products have context-specific experimental support?", "Which expression and receptor-detection datasets provide sufficiently specific evidence for the intended uses?", "Which OPRK1 variant and phenotype claims survive replication and experiments that distinguish association from causation?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }